Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran.

HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts

Occupational Exposure to Sharp Tools in Emergency Medical Service Staff; an Epidemiologic Study

Introduction: Sharp tools are among the major risk factors for transmission of blood borne infections. Therefore, the present study was carried out with the aim of determining epidemiologic aspects of occupational exposure and injury with sharp tools in emergency medical service (EMS) of Dezfoul, Iran, in 2014-2015. Methods: This cross-sectional study was carried out on 140 EMS staff who met the inclusion criteria, using census method. The tool used for data gathering was a questionnaire prepared by the researcher including demographic and personal health data, prevalence and cause of injury with sharp tools, knowledge, mental state, reporting exposure, measures taken, and follow-ups. Data were analyzed using statistical tests such as chi square. Results: Overall, 75% of the participants had been exposed to sharp tools at least once in the past year. Most injuries had occurred during venipuncture of the patient (41.09%). 54.2% of all exposures had happened during transfer. In addition, sadly, 63.9% of the exposures of the staff to patients’ infected secretions were not reported. 63% of injuries with sharp objects had occurred in the night shift. There was a correlation between working experience and frequency of exposure (p=0.02, r=0.19). Conclusion: The results of the present study are indicative of the high occupational exposure to sharp tools among staff of the studied EMS, a significant number of which had not been reported

Evolutionary parameters and their 95% BCIs.

<p>Evolutionary parameters and their 95% BCIs.</p

Genome structure of HIV-1 CRF35_AD.

<p>In this recombinant lineage, subtype D fragments are found within the <i>gag</i>, <i>pol</i>, and <i>env</i> genomic regions, in a genomic background that matches subtype A1. We created four non-overlapping alignments, each of which belonged to one parental lineage of the CRF35_AD only. These alignments include <i>gag</i>_1, <i>gag</i>_2, <i>pol</i>_1, and <i>pol</i>_2. From the <i>pol</i>_1 alignment, which mainly covers parental D fragments, the A1 sections were removed, and the remaining D sections were concatenated. A similar approach was taken to remove parental D section from the <i>pol</i>_2 alignment, which mainly covers parental A1 fragments. Details of nucleotide positions related to these alignments can be found in the Methods.</p

Time-scaled Bayesian MCC trees of the HIV-1 CRF35_AD.

<p><b>(a) <i>gag</i>_1; (b) <i>gag</i>_2; (c) <i>pol</i>_1; (d) <i>pol_2</i>.</b> Key nodes with a posterior clade credibility of 0.7 or greater are marked with black rectangles. Most probable location state and its Posterior State Probability (PSP) are indicated in front of the nodes, corresponding to between-country migration events of CRF35_AD. These nodes are highlighted in Yellow (for Iran → Afghanistan transmission), green (for Afghanistan → Iran transmission), and gray (for Kenya → USA transmission). A highly supported subtype A1 cluster indicating transmission from Afghan refugees to Native Pakistanis is highlighted in blue (Part b). Other parental A1 or D sequences are collapsed for visual clarity. To the upper left of all phylogenies is a bar chart indicating posterior probabilities for the location states of the root of the CRF35_AD_{Afghan-Iranian} cluster (node A). The color code is indicated in the legend, on the lower left corner. <b>PSP:</b> Posterior State Probability; <b>A1:</b> HIV-1 subtype A1; <b>D:</b> HIV-1 subtype D; <b>AF:</b> Afghanistan; <b>IR:</b> Iran; <b>AF refugees</b> _<b>PK</b><b>:</b> Afghan refugees living in Pakistan; <b>BJD:</b> Boroujerd; <b>HE:</b> Herat; <b>KB:</b> Kabul; <b>KE:</b> Kenya; <b>KSH:</b> Kermanshah; <b>MSH:</b> Mashhad; <b>PK:</b> Pakistan; <b>SDJ:</b> Sanandaj; <b>SHZ:</b> Shiraz; <b>TEH:</b> Tehran; <b>UG:</b> Uganda.</p